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- PDB-4okb: Crystal structure of W741L-AR-LBD bound with co-regulator peptide -

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Basic information

Entry
Database: PDB / ID: 4okb
TitleCrystal structure of W741L-AR-LBD bound with co-regulator peptide
Components
  • Androgen receptor
  • Protein BUD31 homolog
KeywordsHORMONE RECEPTOR/PEPTIDE / Alpha-helix / Hormone/growth Factor Receptor / Phosphorylation / HORMONE RECEPTOR-PEPTIDE complex / signal transduction
Function / homology
Function and homology information


male somatic sex determination / : / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / intracellular receptor signaling pathway / tertiary branching involved in mammary gland duct morphogenesis ...male somatic sex determination / : / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / intracellular receptor signaling pathway / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / androgen binding / Leydig cell differentiation / regulation of systemic arterial blood pressure / epithelial cell morphogenesis / prostate gland growth / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / membraneless organelle assembly / prostate gland epithelium morphogenesis / cellular response to testosterone stimulus / positive regulation of androgen receptor activity / RNA polymerase II general transcription initiation factor binding / U2-type catalytic step 2 spliceosome / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / positive regulation of transcription by RNA polymerase III / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / seminiferous tubule development / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / estrogen receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / mRNA Splicing - Major Pathway / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / nuclear receptor coactivator activity / nuclear receptor binding / negative regulation of extrinsic apoptotic signaling pathway / G protein-coupled receptor activity / positive regulation of cell differentiation / molecular condensate scaffold activity / spliceosomal complex / SUMOylation of intracellular receptors / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / multicellular organism growth / mRNA splicing, via spliceosome / beta-catenin binding / transcription coactivator binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / MAPK cascade / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ATPase binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / signaling receptor binding / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Androgen receptor / BUD31/G10-related, conserved site / Androgen receptor / G10 protein signature 1. / G10 protein signature 2. / G10 protein / Pre-mRNA-splicing factor BUD31 / : / Retinoid X Receptor / Retinoid X Receptor ...Androgen receptor / BUD31/G10-related, conserved site / Androgen receptor / G10 protein signature 1. / G10 protein signature 2. / G10 protein / Pre-mRNA-splicing factor BUD31 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
R-BICALUTAMIDE / Androgen receptor / Protein BUD31 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLiu, J.S. / Hsu, C.L. / Wu, W.G.
CitationJournal: Mol Oncol / Year: 2014
Title: Identification of a new androgen receptor (AR) co-regulator BUD31 and related peptides to suppress wild-type and mutated AR-mediated prostate cancer growth via peptide screening and X-ray structure analysis.
Authors: Hsu, C.L. / Liu, J.S. / Wu, P.L. / Guan, H.H. / Chen, Y.L. / Lin, A.C. / Ting, H.J. / Pang, S.T. / Yeh, S.D. / Ma, W.L. / Chen, C.J. / Wu, W.G. / Chang, C.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Androgen receptor
B: Protein BUD31 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5594
Polymers31,0322
Non-polymers5262
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-19 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.243, 66.554, 69.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Androgen receptor / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 29015.035 Da / Num. of mol.: 1 / Fragment: ligand binding doamin / Mutation: W741L, R760A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P10275
#2: Protein/peptide Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 2017.396 Da / Num. of mol.: 1 / Fragment: UNP residues 56-70 / Mutation: I70Y / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P41223
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-198 / R-BICALUTAMIDE / (2R)-N-[4-CYANO-3-(TRIFLUOROMETHYL)PHENYL]-3-[(4-FLUOROPHENYL)SULFONYL]-2-HYDROXY-2-METHYLPROPANAMIDE


Mass: 430.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14F4N2O4S / Comment: medication, hormone*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M magnesium sulphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→29 Å / Num. all: 5855 / Num. obs: 5840 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 17
Reflection shellResolution: 2.96→3.07 Å / Mean I/σ(I) obs: 4.26 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OJB

4ojb


Resolution: 2.95→28.66 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.893 / SU B: 21.163 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25962 264 4.5 %RANDOM
Rwork0.16494 ---
obs0.16936 5546 99.11 %-
all-5859 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.705 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å2-0 Å2
2---2.34 Å2-0 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.95→28.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 34 20 2091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192121
X-RAY DIFFRACTIONr_bond_other_d0.0010.022046
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9732868
X-RAY DIFFRACTIONr_angle_other_deg0.80334687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72223.57198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02415374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8941512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212333
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02521
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.955→3.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 17 -
Rwork0.236 377 -
obs--91.2 %

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